swMATH ID: 26855
Software Authors: Doytchinova, I.A.; Flower, D.R.
Description: VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines. BACKGROUND: Vaccine development in the post-genomic era often begins with the in silico screening of genome information, with the most probable protective antigens being predicted rather than requiring causative microorganisms to be grown. Despite the obvious advantages of this approach–such as speed and cost efficiency–its success remains dependent on the accuracy of antigen prediction. Most approaches use sequence alignment to identify antigens. This is problematic for several reasons. Some proteins lack obvious sequence similarity, although they may share similar structures and biological properties. The antigenicity of a sequence may be encoded in a subtle and recondite manner not amendable to direct identification by sequence alignment. The discovery of truly novel antigens will be frustrated by their lack of similarity to antigens of known provenance. To overcome the limitations of alignment-dependent methods, we propose a new alignment-free approach for antigen prediction, which is based on auto cross covariance (ACC) transformation of protein sequences into uniform vectors of principal amino acid properties. RESULTS: Bacterial, viral and tumour protein datasets were used to derive models for prediction of whole protein antigenicity. Every set consisted of 100 known antigens and 100 non-antigens. The derived models were tested by internal leave-one-out cross-validation and external validation using test sets. An additional five training sets for each class of antigens were used to test the stability of the discrimination between antigens and non-antigens. The models performed well in both validations showing prediction accuracy of 70
Homepage: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-8-4
Related Software: I-TASSER; Euk-PLoc; SVM-Prot; HIVcleave; EzyPred; Signal-3L; MITOPRED; Signal-CF; GPCR-CA; ProtIdent; Memtype-2L; Cell-PLoc; Frustratometer; STRING; BLAST; PSI-BLAST; MUSCLE; QMEAN; Bcepred
Cited in: 3 Publications

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